R Markdown test rmd

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1 data prep spatial layers

read in some data A and data B. Modify some things, and save as layer 1.

2 data prep other layers

This sources a script that modifies another new layer (tableC) and saves it as table2 and table3, external to the direct Rmd path. It also sources a separate script that reads a previously-saved layer (table 1) and gapfills, saving as table1a.

3 model

sourced script reads in layers 1a, 2, and 3, and does some stuff, and saves the results as layers D and E.

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4 The next section (below the divider) is the footer, knitted as a child

The code for the R code chunk header looks like this:

{r child = file.path(dir_git, 'src/templates/ohibc_prov_ftr.Rmd')}

Note that it is executed as if it were just part of this main document; it numbers the section (“Provenance”) as a continuation of the numbering, and the variables are evaluated in the environment of the main document.

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5 Provenance

• Run ID: 33 (695c1a2); run tag: “standard run”
• Run elapsed time: 23.476 seconds; run memory usage: NA MB
• System info: System: Linux, Release: 4.4.0-16-generic. Machine: x86_64. User: ohara.
• Session info
  • R version: R version 3.2.5 (2016-04-14), Platform: x86_64-pc-linux-gnu, Running under: Ubuntu 14.04.4 LTS.
  • Attached base packages: stats, graphics, grDevices, utils, datasets, methods, base
  • Other attached packages: stringr_1.0.0, readr_0.2.2, dplyr_0.4.3

## pre-main prep time: 5 ms

Provenance summary for run 33 (695c1a2): standard run (Fri May 6 12:14:26 2016)

file_name	file_dir	filetype	uncomm_chgs	commit_hash
table1a.csv	~/github/ohibc/rmd_testing	input	FALSE	874af4f
table1.csv	~/github/ohibc/rmd_testing	input	FALSE	874af4f
table2.csv	~/github/ohibc/rmd_testing	input	FALSE	874af4f
table3.csv	~/github/ohibc/rmd_testing	input	FALSE	874af4f
tableA2.csv	~	input	TRUE	NA
tableA.csv	~/github/ohibc/rmd_testing	input	FALSE	2062ccb
tableB.csv	~/github/ohibc/rmd_testing	input	FALSE	0bb1fa0
tableC.csv	~/github/ohibc/rmd_testing	input	FALSE	0bb1fa0
table1a.csv	~/github/ohibc/rmd_testing	output	FALSE	874af4f
table1.csv	~/github/ohibc/rmd_testing	output	FALSE	874af4f
table2.csv	~/github/ohibc/rmd_testing	output	FALSE	874af4f
table3.csv	~/github/ohibc/rmd_testing	output	FALSE	874af4f
tableD.csv	~/github/ohibc/rmd_testing	output	FALSE	874af4f
tableE.csv	~/github/ohibc/rmd_testing	output	FALSE	874af4f
0_sample_script.Rmd	~/github/ohibc/rmd_testing	parent_script	FALSE	15c4aeb
1a_gapfill.R	~/github/ohibc/rmd_testing	sourced_script	FALSE	725220e
1_data_prep_sample.R	~/github/ohibc/rmd_testing	sourced_script	FALSE	c265b26
2_model_sample.R	~/github/ohibc/rmd_testing	sourced_script	FALSE	725220e